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cannot open file when knit rmarkdown #187

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xf15 opened this issue Dec 28, 2021 · 1 comment
Open

cannot open file when knit rmarkdown #187

xf15 opened this issue Dec 28, 2021 · 1 comment

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@xf15
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xf15 commented Dec 28, 2021

in my rmd r chunk, i have

name = "data/_interface_eyetracking_2021_Dec_23_2024.hdf5"

file_h5 = hdf5r::H5File$new(name, mode = c("r"))

i can run it in chunk fine, open file, and do things, but when i knit, i get

 Quitting from lines 48-74 (preprocess.Rmd) 
Error in H5File.open(filename, mode, file_create_pl, file_access_pl) : 
  HDF5-API Errors:
    error #000: ../../src/hdf5-1.12.0/src/H5F.c in H5Fopen(): line 793: unable to open file
        class: HDF5
        major: File accessibility
        minor: Unable to open file

    error #001: ../../src/hdf5-1.12.0/src/H5VLcallback.c in H5VL_file_open(): line 3500: open failed
        class: HDF5
        major: Virtual Object Layer
        minor: Can't open object

    error #002: ../../src/hdf5-1.12.0/src/H5VLcallback.c in H5VL__file_open(): line 3465: open failed
        class: HDF5
        major: Virtual Object Layer
        minor: Can't open object

    error #003: ../../src/hdf5-1.12.0/src/H5VLnative_file.c in H5VL__native_file_open(): line 100: unable to open file
        class: HDF5
        major: File accessibility
        minor: Unable to open file

    error #004: ../../src/hdf5-1.12.0/src/H5Fint.c in H5F_open(): line 1622: unable to lock the file
        class: HDF5
        major: File accessibility
        minor: Unable to open file

    error

in my top chunk, i also have library(hdf5r)

@xf15
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xf15 commented Dec 28, 2021

if i copy hdf5 file to the same dir as the rmd file, change path accordingly, it opens ...
i am on mac
i also tried file.path, doesn't help

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